No, just in time! I have the game minimized now and I'm trying to decide how to go about this. It's all excellent information. The toughest challenge for me is deciding what to do with an excellent site when it could be made into anything I want it to be!
Most of the time, a city site is going to be better at one thing than another, which is almost always the determining factor to me as for what it will be.
In the rare cases I find a city that truly can be great at anything, I compare what the rest of the empire has available to it. So if every other city has poor production (or I only have one other production city), then I know the empire needs a good production city and the city is made into a production centre.
Likewise, if every other city is a production city, I have no GP Farm yet or my economy is in the toilet, then the city becomes a GP Farm or Cottage spam city.
when trying to set up a Hybrid economy, is it best to have some commerce cities and some specialist cites, or is it best to have cities that work commerce tiles and run specialists?
I typically don't like to run specialists and cottages in the same city at the same time. I don't know if I have a good reason for this or if it's just personal preference, but it's what I'm accustomed to.
If you aren't running Caste System, then you have no choice but to run specialists and work cottages in the same city.
I think one of the reasons why I segregate my commerce and specialist cities is because I prefer to exclusively run merchants in my specialist cities (non-GP Farm). I think I like to do this because it all but guarantees I'll get a late-game Great Merchant once one of the specialist cities finally catches up to the GP Farm and makes a Great Person.
Knowing I'll be running gold-heavy in those cities, I feel it's easier for me to justify prioritizing gold-boosting buildings there.
Quechua wrote an article on
Gold, Beakers, and Deficit Research in which he showed an example where running a Merchant instead of a Scientist was actually
better for the overall science rate, because it allowed the slider to be increased.
At any rate, I find the only times I run truly hybrid (cottage & specialists) cities is when the city has decent production but not enough to be stelar. I run specialists roughly equivalent to the number of production tiles I have so that when production is called for, the city can keep working its cottages but still get the production it needs from the 'off-duty' specialists.
-- my 2